1
|
Byndloss M, Devkota S, Duca F, Hendrik Niess J, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes Care 2024; 47:1491-1508. [PMID: 38996003 PMCID: PMC11362125 DOI: 10.2337/dci24-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 07/14/2024]
Abstract
This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
Collapse
Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Suzanne Devkota
- Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
| |
Collapse
|
2
|
Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes 2024; 73:1391-1410. [PMID: 38912690 PMCID: PMC11333376 DOI: 10.2337/dbi24-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
Collapse
Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Suzanne Devkota
- Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
| |
Collapse
|
3
|
Liu Y, Wang Z, Li K, Song R, Xu Z, Yu T, Wang J, Feng X, Chen H. Positive-Charge-Based Small Molecule Dyes for Gut Microbiota Fluorescent Imaging. ACS OMEGA 2024; 9:36371-36379. [PMID: 39220500 PMCID: PMC11360029 DOI: 10.1021/acsomega.4c03727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/07/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
As one of the research hotspots in recent years, gut microbiota have been proven to be closely related to host metabolism, nutrient absorption, and immune regulation. However, there are still many urgent issues in the research of gut microbiota, such as the localization and tracking of gut microbiota. In this research, two new fluorescent probes, EF and 6F, were developed by optimizing the structure of the positron salt small molecule probe F16. In vitro labeling experiments showed that EF and 6F can quickly label Gram-positive bacteria, Staphylococcus aureus and Lactobacillus reuteri, as well as Gram-negative bacteria, Escherichia coli and Salmonella pullorum. Meanwhile, EF and 6F have little bacterial toxicity and are used at a maximum concentration of 200 μM. Compared with EF, 6F has better hydrophilicity and stronger fluorescence characteristics in aqueous solutions, making it more suitable for imaging within gut microbiota populations. The results of in vivo imaging experiments indicate that EF and 6F can label and image the intestinal microbiota colonized by the mouse intestinal mucosal epithelium without causing any damage to intestinal tissue. Compared with commercially available MitoTracker dyes and fluorescein 5-isothiocyanate (FITC) dyes, EF and 6F exhibit better biocompatibility. Therefore, the compounds EF and 6F synthesized in this study are novel small molecule probes suitable for imaging gut microbiota, providing a better probe selection for exploring complex gut microbiota.
Collapse
Affiliation(s)
- Yue Liu
- State
Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious
Diseases, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhiming Wang
- State
Key Laboratory of Chemical Biology, Molecular Imaging Center, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Ke Li
- State
Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious
Diseases, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Ruihu Song
- State
Key Laboratory of Chemical Biology, Molecular Imaging Center, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Zhiqiang Xu
- State
Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious
Diseases, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Tianhe Yu
- State
Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious
Diseases, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jing Wang
- Radiology
Department, the First Hospital of Jilin
University, Changchun 130021, China
| | - Xin Feng
- State
Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious
Diseases, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hao Chen
- State
Key Laboratory of Chemical Biology, Molecular Imaging Center, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| |
Collapse
|
4
|
Jin W, Guo C. Genetic manipulations of nonmodel gut microbes. IMETA 2024; 3:e216. [PMID: 39135697 PMCID: PMC11316930 DOI: 10.1002/imt2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 08/15/2024]
Abstract
Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The "bottleneck" preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step-by-step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram-negative Bacteroidia and Gram-positive Clostridia organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases.
Collapse
Affiliation(s)
- Wen‐Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Friedman Center for Nutrition and Inflammation, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
| | - Chun‐Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Friedman Center for Nutrition and Inflammation, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Joan and Sanford I. Weill Department of Medicine, Gastroenterology and Hepatology Division, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Department of Microbiology and Immunology, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
| |
Collapse
|
5
|
Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetologia 2024:10.1007/s00125-024-06198-1. [PMID: 38910152 DOI: 10.1007/s00125-024-06198-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
Collapse
Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne Devkota
- Cedars-Sinai Medical Center, Human Microbiome Research Institute, Los Angeles, CA, USA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain.
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| |
Collapse
|
6
|
Armbruster KM, Jiang J, Sartorio MG, Scott NE, Peterson JM, Sexton JZ, Feldman MF, Koropatkin NM. Identification and Characterization of the Lipoprotein N-acyltransferase in Bacteroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596883. [PMID: 38853980 PMCID: PMC11160734 DOI: 10.1101/2024.05.31.596883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Members of the Bacteroidota compose a large portion of the human gut microbiota, contributing to overall gut health via the degradation of various polysaccharides. This process is facilitated by lipoproteins, globular proteins anchored to the cell surface by a lipidated N-terminal cysteine. Despite their importance, lipoprotein synthesis by these bacteria is understudied. In E. coli, the α-amino linked lipid of lipoproteins is added by the lipoprotein N-acyltransferase Lnt. Herein, we have identified a protein distinct from Lnt responsible for the same process in Bacteroides, named lipoprotein N-acyltransferase in Bacteroides (Lnb). Deletion of Lnb yields cells that synthesize diacylated lipoproteins, with impacts on cell viability and morphology, growth on polysaccharides, and protein composition of membranes and outer membrane vesicles (OMVs). Our results not only challenge the accepted paradigms of lipoprotein biosynthesis in Gram-negative bacteria, but also support the establishment of a new family of lipoprotein N-acyltransferases.
Collapse
Affiliation(s)
- Krista M Armbruster
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jiawen Jiang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Mariana G Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, 3000, Australia
| | - Jenna M Peterson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| |
Collapse
|
7
|
Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
Collapse
Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| |
Collapse
|
8
|
Raev SA, Kick MK, Chellis M, Amimo JO, Saif LJ, Vlasova AN. Histo-Blood Group Antigen-Producing Bacterial Cocktail Reduces Rotavirus A, B, and C Infection and Disease in Gnotobiotic Piglets. Viruses 2024; 16:660. [PMID: 38793542 PMCID: PMC11125826 DOI: 10.3390/v16050660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
The suboptimal performance of rotavirus (RV) vaccines in developing countries and in animals necessitates further research on the development of novel therapeutics and control strategies. To initiate infection, RV interacts with cell-surface O-glycans, including histo-blood group antigens (HBGAs). We have previously demonstrated that certain non-pathogenic bacteria express HBGA- like substances (HBGA+) capable of binding RV particles in vitro. We hypothesized that HBGA+ bacteria can bind RV particles in the gut lumen protecting against RV species A (RVA), B (RVB), and C (RVC) infection in vivo. In this study, germ-free piglets were colonized with HBGA+ or HBGA- bacterial cocktail and infected with RVA/RVB/RVC of different genotypes. Diarrhea severity, virus shedding, immunoglobulin A (IgA) Ab titers, and cytokine levels were evaluated. Overall, colonization with HBGA+ bacteria resulted in reduced diarrhea severity and virus shedding compared to the HBGA- bacteria. Consistent with our hypothesis, the reduced severity of RV disease and infection was not associated with significant alterations in immune responses. Additionally, colonization with HBGA+ bacteria conferred beneficial effects irrespective of the piglet HBGA phenotype. These findings are the first experimental evidence that probiotic performance in vivo can be improved by including HBGA+ bacteria, providing decoy epitopes for broader/more consistent protection against diverse RVs.
Collapse
Affiliation(s)
- Sergei A. Raev
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.A.R.); (M.K.K.); (M.C.); (L.J.S.)
| | - Maryssa K. Kick
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.A.R.); (M.K.K.); (M.C.); (L.J.S.)
| | - Maria Chellis
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.A.R.); (M.K.K.); (M.C.); (L.J.S.)
| | | | - Linda J. Saif
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.A.R.); (M.K.K.); (M.C.); (L.J.S.)
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.A.R.); (M.K.K.); (M.C.); (L.J.S.)
| |
Collapse
|
9
|
Wong JPH, Chillier N, Fischer-Stettler M, Zeeman SC, Battin TJ, Persat A. Bacteroides thetaiotaomicron metabolic activity decreases with polysaccharide molecular weight. mBio 2024; 15:e0259923. [PMID: 38376161 PMCID: PMC10936149 DOI: 10.1128/mbio.02599-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
The human colon hosts hundreds of commensal bacterial species, many of which ferment complex dietary carbohydrates. To transform these fibers into metabolically accessible compounds, microbes often express a series of dedicated enzymes homologous to the starch utilization system (Sus) encoded in polysaccharide utilization loci (PULs). The genome of Bacteroides thetaiotaomicron (Bt), a common member of the human gut microbiota, encodes nearly 100 PULs, conferring a strong metabolic versatility. While the structures and functions of individual enzymes within the PULs have been investigated, little is known about how polysaccharide complexity impacts the function of Sus-like systems. We here show that the activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth. We demonstrate the effect of size-dependent metabolism in the context of dextran metabolism driven by the specific utilization system PUL48. We find that as the molecular weight of dextran increases, Bt growth rate decreases and lag time increases. At the enzymatic level, the dextranase BT3087, a glycoside hydrolase (GH) belonging to the GH family 66, is the main GH for dextran utilization, and BT3087 and BT3088 contribute to Bt dextran metabolism in a size-dependent manner. Finally, we show that the polysaccharide size-dependent metabolism of Bt impacts its metabolic output in a way that modulates the composition of a producer-consumer community it forms with Bacteroides fragilis. Altogether, our results expose an overlooked aspect of Bt metabolism that can impact the composition and diversity of microbiota. IMPORTANCE Polysaccharides are complex molecules that are commonly found in our diet. While humans lack the ability to degrade many polysaccharides, their intestinal microbiota contain bacterial commensals that are versatile polysaccharide utilizers. The gut commensal Bacteroides thetaiotaomicron dedicates roughly 20% of their genomes to the expression of polysaccharide utilization loci for the broad range utilization of polysaccharides. Although it is known that different polysaccharide utilization loci are dedicated to the degradation of specific polysaccharides with unique glycosidic linkages and monosaccharide compositions, it is often overlooked that specific polysaccharides may also exist in various molecular weights. These different physical attributes may impact their processability by starch utilization system-like systems, leading to differing growth rates and nutrient-sharing properties at the community level. Therefore, understanding how molecular weight impacts utilization by gut microbe may lead to the potential design of novel precision prebiotics.
Collapse
Affiliation(s)
- Jeremy P. H. Wong
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Noémie Chillier
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | | | - Tom J. Battin
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
10
|
Pardue EJ, Sartorio MG, Jana B, Scott NE, Beatty WL, Ortiz-Marquez JC, Van Opijnen T, Hsu FF, Potter RF, Feldman MF. Dual membrane-spanning anti-sigma factors regulate vesiculation in Bacteroides thetaiotaomicron. Proc Natl Acad Sci U S A 2024; 121:e2321910121. [PMID: 38422018 PMCID: PMC10927553 DOI: 10.1073/pnas.2321910121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024] Open
Abstract
Bacteroidota are abundant members of the human gut microbiota that shape the enteric landscape by modulating host immunity and degrading dietary- and host-derived glycans. These processes are mediated in part by Outer Membrane Vesicles (OMVs). Here, we developed a high-throughput screen to identify genes required for OMV biogenesis and its regulation in Bacteroides thetaiotaomicron (Bt). We identified a family of Dual membrane-spanning anti-sigma factors (Dma) that control OMV biogenesis. We conducted molecular and multiomic analyses to demonstrate that deletion of Dma1, the founding member of the Dma family, modulates OMV production by controlling the activity of the ECF21 family sigma factor, Das1, and its downstream regulon. Dma1 has a previously uncharacterized domain organization that enables Dma1 to span both the inner and outer membrane of Bt. Phylogenetic analyses reveal that this common feature of the Dma family is restricted to the phylum Bacteroidota. This study provides mechanistic insights into the regulation of OMV biogenesis in human gut bacteria.
Collapse
Affiliation(s)
- Evan J. Pardue
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Mariana G. Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Biswanath Jana
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC3000, Australia
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | | | | | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, Saint Louis, MO63110
| | - Robert F. Potter
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO63110
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| |
Collapse
|
11
|
Fancy N, Nitin, Kniffen D, Melvin M, Kazemian N, Sadeghi J, Letef CA, D'Aloisio L, Copp AG, Inaba R, Hans G, Jafaripour S, Haskey N, Raman M, Daneshgar P, Chadee K, Ghosh S, Gibson DL, Pakpour S, Zandberg W, Bergstrom KSB. Fecal-adherent mucus is a non-invasive source of primary human MUC2 for structural and functional characterization in health and disease. J Biol Chem 2024; 300:105675. [PMID: 38272223 PMCID: PMC10891339 DOI: 10.1016/j.jbc.2024.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
The O-glycoprotein Mucin-2 (MUC2) forms the protective colon mucus layer. While animal models have demonstrated the importance of Muc2, few studies have explored human MUC2 in similar depth. Recent studies have revealed that secreted MUC2 is bound to human feces. We hypothesized human fecal MUC2 (HF-MUC2) was accessible for purification and downstream structural and functional characterization. We tested this via histologic and quantitative imaging on human fecal sections; extraction from feces for proteomic and O-glycomic characterization; and functional studies via growth and metabolic assays in vitro. Quantitative imaging of solid fecal sections showed a continuous mucus layer of varying thickness along human fecal sections with barrier functions intact. Lectin profiling showed HF-MUC2 bound several lectins but was weak to absent for Ulex europaeus 1 (α1,2 fucose-binding) and Sambucus nigra agglutinin (α2,6 sialic acid-binding), and did not have obvious b1/b2 barrier layers. HF-MUC2 separated by electrophoresis showed high molecular weight glycoprotein bands (∼1-2 MDa). Proteomics and Western analysis confirmed the enrichment of MUC2 and potential MUC2-associated proteins in HF-MUC2 extracts. MUC2 O-glycomics revealed diverse fucosylation, moderate sialylation, and little sulfation versus porcine colonic MUC2 and murine fecal Muc2. O-glycans were functional and supported the growth of Bacteroides thetaiotaomicron (B. theta) and short-chain fatty acid (SCFA) production in vitro. MUC2 could be similarly analyzed from inflammatory bowel disease stools, which displayed an altered glycomic profile and differential growth and SCFA production by B. theta versus healthy samples. These studies describe a new non-invasive platform for human MUC2 characterization in health and disease.
Collapse
Affiliation(s)
- Noah Fancy
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Nitin
- Chemistry, University of British Columbia-Okanagan, Kelowna, Canada
| | - Darrek Kniffen
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Mackenzie Melvin
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Negin Kazemian
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Javad Sadeghi
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Clara A Letef
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Leah D'Aloisio
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Amanda G Copp
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Rain Inaba
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Geetkamal Hans
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Simin Jafaripour
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Natasha Haskey
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Maitreyi Raman
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | | | - Kris Chadee
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sanjoy Ghosh
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Deanna L Gibson
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Sepideh Pakpour
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Wesley Zandberg
- Chemistry, University of British Columbia-Okanagan, Kelowna, Canada
| | | |
Collapse
|
12
|
Kim TH, Ju K, Kim SK, Woo SG, Lee JS, Lee CH, Rha E, Shin J, Kwon KK, Lee H, Kim H, Lee SG, Lee DH. Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species. ACS Synth Biol 2024; 13:648-657. [PMID: 38224571 DOI: 10.1021/acssynbio.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The genus Bacteroides, a predominant group in the human gut microbiome, presents significant potential for microbiome engineering and the development of live biotherapeutics aimed at treating gut diseases. Despite its promising capabilities, tools for effectively engineering Bacteroides species have been limited. In our study, we have made a breakthrough by identifying novel signal peptides in Bacteroides thetaiotaomicron and Akkermansia muciniphila. These peptides facilitate efficient protein transport across cellular membranes in Bacteroides, a critical step for therapeutic applications. Additionally, we have developed an advanced episomal plasmid system. This system demonstrates superior protein secretion capabilities compared to traditional chromosomal integration plasmids, making it a vital tool for enhancing the delivery of therapeutic proteins in Bacteroides species. Initially, the stability of this episomal plasmid posed a challenge; however, we have overcome this by incorporating an essential gene-based selection system. This novel strategy not only ensures plasmid stability but also aligns with the growing need for antibiotic-free selection methods in clinical settings. Our work, therefore, not only provides a more robust secretion system for Bacteroides but also sets a new standard for the development of live biotherapeutics.
Collapse
Affiliation(s)
- Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Kowoon Ju
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si 56212, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
13
|
Meyerowitz JT, Larsson EM, Murray RM. Development of Cell-Free Transcription-Translation Systems in Three Soil Pseudomonads. ACS Synth Biol 2024; 13:530-537. [PMID: 38319019 DOI: 10.1021/acssynbio.3c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
In vitro transcription-translation (TX-TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX-TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX-TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX-TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX-TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design-build-test cycle.
Collapse
Affiliation(s)
- Joseph T Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Elin M Larsson
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| |
Collapse
|
14
|
Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
Collapse
Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
| |
Collapse
|
15
|
Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction. Cell Rep 2024; 43:113517. [PMID: 38142397 DOI: 10.1016/j.celrep.2023.113517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
Collapse
Affiliation(s)
- Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Mary Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nazgul Sakenova
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tümay Capraz
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentine Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Zimmerman
- Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Justin L Sonnenburg
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
16
|
Larsson EM, Murray RM, Newman DK. Engineering the Soil Bacterium Pseudomonas synxantha 2-79 into a Ratiometric Bioreporter for Phosphorus Limitation. ACS Synth Biol 2024; 13:384-393. [PMID: 38165130 DOI: 10.1021/acssynbio.3c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25-100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8-8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter's performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.
Collapse
Affiliation(s)
- Elin M Larsson
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, United States
| | - Dianne K Newman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
17
|
Juodeikis R, Martins C, Saalbach G, Richardson J, Koev T, Baker DJ, Defernez M, Warren M, Carding SR. Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles. J Extracell Vesicles 2024; 13:e12406. [PMID: 38240185 PMCID: PMC10797578 DOI: 10.1002/jev2.12406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/24/2023] [Accepted: 01/01/2024] [Indexed: 01/22/2024] Open
Abstract
Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.
Collapse
Affiliation(s)
- Rokas Juodeikis
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | | | | | | | - Trey Koev
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- School of PharmacyUniversity of East AngliaNorwichUK
| | - Dave J. Baker
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Marianne Defernez
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Martin Warren
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- School of BiosciencesUniversity of KentCanterburyUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Simon R. Carding
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| |
Collapse
|
18
|
Hill CA, Casterline BW, Valguarnera E, Hecht AL, Shepherd ES, Sonnenburg JL, Bubeck Wardenburg J. Bacteroides fragilis toxin expression enables lamina propria niche acquisition in the developing mouse gut. Nat Microbiol 2024; 9:85-94. [PMID: 38168616 PMCID: PMC11214347 DOI: 10.1038/s41564-023-01559-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Bacterial toxins are well-studied virulence factors; however, recent studies have revealed their importance in bacterial niche adaptation. Enterotoxigenic Bacteroides fragilis (ETBF) expresses B. fragilis toxin (BFT) that we hypothesized may contribute to both colonic epithelial injury and niche acquisition. We developed a vertical transmission model for ETBF in mice that showed that BFT enabled ETBF to access a lamina propria (LP) niche during colonic microbiome development that was inaccessible to non-toxigenic B. fragilis. LP entry by ETBF required BFT metalloprotease activity, and showed temporal restriction to the pre-weaning period, dependent on goblet-cell-associated passages. In situ single-cell analysis showed bft expression at the apical epithelial surface and within the LP. BFT expression increased goblet cell number and goblet-cell-associated passage formation. These findings define a paradigm by which bacterial toxin expression specifies developmental niche acquisition, suggesting that a selective advantage conferred by a toxin may impact long-term host health.
Collapse
Affiliation(s)
- Craig A Hill
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Benjamin W Casterline
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
- Department of Dermatology, University of Missouri School of Medicine, Columbia, MO, USA
| | | | - Aaron L Hecht
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
- Division of Gastroenterology and Hepatology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | |
Collapse
|
19
|
Pardue EJ, Feldman MF. Screening for Genes Involved in Outer Membrane Vesicle Biogenesis in Bacteroides thetaiotaomicron. Methods Mol Biol 2024; 2843:57-71. [PMID: 39141294 DOI: 10.1007/978-1-0716-4055-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Bacteroides spp. are prominent gut commensals that are believed to modulate the intestinal environment, in part, by producing outer membrane vesicles (OMVs). Bacteroides OMVs have been ascribed many functions in vitro, but the genetic underpinnings behind OMV biogenesis and regulation are unclear. Understanding the mechanism of OMV biogenesis is required to determine the importance of Bacteroides OMVs in vivo. Here, we describe our methodology for screening Bacteroides thetaiotaomicron VPI-5482 to identify genes required for OMV biogenesis and regulation in a high-throughput format. This protocol is easily adaptable and can potentially be employed to further our knowledge of OMV biogenesis in other bacteria.
Collapse
Affiliation(s)
- Evan J Pardue
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
20
|
Nemet I, Funabashi M, Li XS, Dwidar M, Sangwan N, Skye SM, Romano KA, Cajka T, Needham BD, Mazmanian SK, Hajjar AM, Rey FE, Fiehn O, Tang WHW, Fischbach MA, Hazen SL. Microbe-derived uremic solutes enhance thrombosis potential in the host. mBio 2023; 14:e0133123. [PMID: 37947418 PMCID: PMC10746243 DOI: 10.1128/mbio.01331-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Alterations in gut microbial composition and function have been linked to numerous diseases. Identifying microbial pathways responsible for producing molecules that adversely impact the host is an important first step in the development of therapeutic interventions. Here, we first use large-scale clinical observations to link blood levels of defined microbial products to cardiovascular disease risks. Notably, the previously identified uremic toxins p-cresol sulfate and indoxyl sulfate were shown to predict 5-year mortality risks. After identifying the microbes and microbial enzymes involved in the generation of these uremic toxins, we used bioengineering technologies coupled with colonization of germ-free mice to show that the gut microbial genes that generate p-cresol and indole are sufficient to confer p-cresol sulfate and indoxyl sulfate formation, and a pro-thrombotic phenotype in vivo. The findings and tools developed serve as a critical step in both the study and targeting of these gut microbial pathways in vivo.
Collapse
Affiliation(s)
- Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Masanori Funabashi
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
- ChEM-H Institute, Stanford University, Stanford, California, USA
| | - Xinmin S. Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mohammed Dwidar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah M. Skye
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kymberleigh A. Romano
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tomas Cajka
- West Coast Metabolomics Center, University of California, Davis, California, USA
| | - Brittany D. Needham
- Departments of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Sarkis K. Mazmanian
- Departments of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Adeline M. Hajjar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, California, USA
| | - W. H. Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael A. Fischbach
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
- ChEM-H Institute, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Stanley L. Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, Ohio, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio, USA
| |
Collapse
|
21
|
Yeh YH, Kelly VW, Pour RR, Sirk SJ. A molecular toolkit for heterologous protein secretion across Bacteroides species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571725. [PMID: 38168418 PMCID: PMC10760143 DOI: 10.1101/2023.12.14.571725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
Collapse
Affiliation(s)
- Yu-Hsuan Yeh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Vince W. Kelly
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Rahman Rahman Pour
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Perlumi, Berkeley, CA 94704, USA
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead Contact
| |
Collapse
|
22
|
Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
Collapse
Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| |
Collapse
|
23
|
Liu B, Garza DR, Gonze D, Krzynowek A, Simoens K, Bernaerts K, Geirnaert A, Faust K. Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis. THE ISME JOURNAL 2023; 17:1940-1952. [PMID: 37670028 PMCID: PMC10579405 DOI: 10.1038/s41396-023-01501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.
Collapse
Affiliation(s)
- Bin Liu
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Daniel Rios Garza
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP 231, Université Libre de Bruxelles, Bvd du Triomphe, B-1050, Bruxelles, Belgium
| | - Anna Krzynowek
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092, Zürich, Switzerland
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium.
| |
Collapse
|
24
|
Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
Collapse
Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
| |
Collapse
|
25
|
Kubiak AM, Claessen L, Zhang Y, Khazaie K, Bailey TS. Refined control of CRISPR-Cas9 gene editing in Clostridium sporogenes: the creation of recombinant strains for therapeutic applications. Front Immunol 2023; 14:1241632. [PMID: 37869009 PMCID: PMC10585264 DOI: 10.3389/fimmu.2023.1241632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023] Open
Abstract
Despite considerable clinical success, the potential of cancer immunotherapy is restricted by a lack of tumour-targeting strategies. Treatment requires systemic delivery of cytokines or antibodies at high levels to achieve clinically effective doses at malignant sites. This is exacerbated by poor penetration of tumour tissue by therapeutic antibodies. High-grade immune-related adverse events (irAEs) occur in a significant number of patients (5-15%, cancer- and therapeutic-dependent) that can lead to lifelong issues and can exclude from treatment patients with pre-existing autoimmune diseases. Tumour-homing bacteria, genetically engineered to produce therapeutics, is one of the approaches that seeks to mitigate these drawbacks. The ability of Clostridium sporogenes to form spores that are unable to germinate in the presence of oxygen (typical of healthy tissue) offers a unique advantage over other vectors. However, the limited utility of existing gene editing tools hinders the development of therapeutic strains. To overcome the limitations of previous systems, expression of the Cas9 protein and the gRNA was controlled using tetracycline inducible promoters. Furthermore, the components of the system were divided across two plasmids, improving the efficiency of cloning and conjugation. Genome integrated therapeutic genes were assayed biochemically and in cell-based functional assays. The potency of these strains was further improved through rationally-conceived gene knock-outs. The new system was validated by demonstrating the efficient addition and deletion of large sequences from the genome. This included the creation of recombinant strains expressing two pro-inflammatory cytokines, interleukin-2 (IL-2) and granulocyte macrophage-colony stimulating factor (GM-CSF), and a pro-drug converting enzyme (PCE). A comparative, temporal in vitro analysis of the integrant strains and their plasmid-based equivalents revealed a substantial reduction of cytokine activity in chromosome-based constructs. To compensate for this loss, a 7.6 kb operon of proteolytic genes was deleted from the genome. The resultant knock-out strains showed an 8- to 10-fold increase in cytokine activity compared to parental strains.
Collapse
Affiliation(s)
- Aleksandra M. Kubiak
- Exomnis Biotech BV, Maastricht, Netherlands
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Luuk Claessen
- Exomnis Biotech BV, Maastricht, Netherlands
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Yanchao Zhang
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Khashayarsha Khazaie
- Department of Immunology and Cancer Biology, Mayo Clinic, Phoenix, AZ, United States
| | - Tom S. Bailey
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
26
|
Madhu B, Miller BM, Levy M. Single-cell analysis and spatial resolution of the gut microbiome. Front Cell Infect Microbiol 2023; 13:1271092. [PMID: 37860069 PMCID: PMC10582963 DOI: 10.3389/fcimb.2023.1271092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Over the past decade it has become clear that various aspects of host physiology, metabolism, and immunity are intimately associated with the microbiome and its interactions with the host. Specifically, the gut microbiome composition and function has been shown to play a critical role in the etiology of different intestinal and extra-intestinal diseases. While attempts to identify a common pattern of microbial dysbiosis linked with these diseases have failed, multiple studies show that bacterial communities in the gut are spatially organized and that disrupted spatial organization of the gut microbiome is often a common underlying feature of disease pathogenesis. As a result, focus over the last few years has shifted from analyzing the diversity of gut microbiome by sequencing of the entire microbial community, towards understanding the gut microbiome in spatial context. Defining the composition and spatial heterogeneity of the microbiome is critical to facilitate further understanding of the gut microbiome ecology. Development in single cell genomics approach has advanced our understanding of microbial community structure, however, limitations in approaches exist. Single cell genomics is a very powerful and rapidly growing field, primarily used to identify the genetic composition of microbes. A major challenge is to isolate single cells for genomic analyses. This review summarizes the different approaches to study microbial genomes at single-cell resolution. We will review new techniques for microbial single cell sequencing and summarize how these techniques can be applied broadly to answer many questions related to the microbiome composition and spatial heterogeneity. These methods can be used to fill the gaps in our understanding of microbial communities.
Collapse
Affiliation(s)
| | | | - Maayan Levy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
27
|
Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
Collapse
Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| |
Collapse
|
28
|
Alker AT, Farrell MV, Aspiras AE, Dunbar TL, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis. mBio 2023; 14:e0150223. [PMID: 37530556 PMCID: PMC10470607 DOI: 10.1128/mbio.01502-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCE Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as Escherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine Pseudoalteromonas bacterium to study their association with its host animal Hydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
Collapse
Affiliation(s)
- Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Morgan V. Farrell
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Alpher E. Aspiras
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tiffany L. Dunbar
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Andriy Fedoriouk
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Jeffrey E. Jones
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Sama R. Mikhail
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Nicholas J. Shikuma
- Department of Biology, San Diego State University, San Diego, California, USA
| |
Collapse
|
29
|
Bailey TS, Hittmeyer P, Zhang Y, Kubiak AM. Streamlined assembly of cloning and genome editing vectors for genus Clostridium. iScience 2023; 26:107484. [PMID: 37599836 PMCID: PMC10432817 DOI: 10.1016/j.isci.2023.107484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/27/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Reported herein is a new set of vectors designed to streamline molecular cloning and genome editing by exploiting modern cloning methods. The new vectors build on the existing pMTL8000 vectors that have been a staple of Clostridium research for more than a decade. The introduction of two pairs of type IIS restriction sites flanking an insulated multiple cloning site in both a cloning vector and a CRISPR-Cas9 gene editing vector enables plasmid construction in a "one-pot" reaction, avoiding the more laborious steps of conventional cloning. A synthetic lacZα expression cassette introduced between the cloning sites enables visual detection of background colonies. In addition, distinct selection markers on each vector permit selection of the desired clones according to antibiotic resistance. An example of strain development using the new vectors is demonstrated.
Collapse
Affiliation(s)
- Tom S. Bailey
- GROW - School for Oncology and Reproduction, Faculty of Health and Medical Life Sciences, Maastricht University, Maastricht, Limburg, the Netherlands
| | - Philip Hittmeyer
- GROW - School for Oncology and Reproduction, Faculty of Health and Medical Life Sciences, Maastricht University, Maastricht, Limburg, the Netherlands
| | - Yanchao Zhang
- GROW - School for Oncology and Reproduction, Faculty of Health and Medical Life Sciences, Maastricht University, Maastricht, Limburg, the Netherlands
| | | |
Collapse
|
30
|
Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
Collapse
Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
| |
Collapse
|
31
|
Abellon-Ruiz J, Jana K, Silale A, Frey AM, Baslé A, Trost M, Kleinekathöfer U, van den Berg B. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides. Nat Commun 2023; 14:4714. [PMID: 37543597 PMCID: PMC10404256 DOI: 10.1038/s41467-023-40427-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
Vitamin B12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B12 outer membrane transporters together with a conserved array of surface-exposed B12-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B12 with high affinities. Closing of the BtuG lid following B12 capture causes destabilisation of the bound B12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.
Collapse
Affiliation(s)
- Javier Abellon-Ruiz
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kalyanashis Jana
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew M Frey
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthias Trost
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|
32
|
Arnold J, Glazier J, Mimee M. Genetic Engineering of Resident Bacteria in the Gut Microbiome. J Bacteriol 2023; 205:e0012723. [PMID: 37382533 PMCID: PMC10367592 DOI: 10.1128/jb.00127-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.
Collapse
Affiliation(s)
- Jack Arnold
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Joshua Glazier
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Mark Mimee
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
33
|
Pardue EJ, Sartorio MG, Jana B, Scott NE, Beatty W, Ortiz-Marquez JC, Van Opijnen T, Hsu FF, Potter R, Feldman MF. Dual Membrane-spanning Anti-Sigma Factors Regulate Vesiculation in Gut Bacteroidota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548920. [PMID: 37503209 PMCID: PMC10369966 DOI: 10.1101/2023.07.13.548920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Bacteroidota are abundant members of the human gut microbiota that shape the enteric landscape by modulating host immunity and degrading dietary- and host-derived glycans. These processes are at least partially mediated by O uter M embrane V esicles (OMVs). In this work, we developed a high-throughput screen to identify genes required for OMV biogenesis and its regulation in Bacteroides thetaiotaomicron ( Bt ). Our screening led us to the identification of a novel family of D ual M embrane-spanning A nti-sigma factors (Dma), which regulate OMV biogenesis in Bt . We employed molecular and multiomic analyses to demonstrate that deletion of Dma1, the founding member of the Dma family, results in hypervesiculation by modulating the expression of NigD1, which belongs to a family of uncharacterized proteins found throughout Bacteroidota. Dma1 has an unprecedented domain organization: it contains a C-terminal β-barrel embedded in the OM; its N-terminal domain interacts with its cognate sigma factor in the cytoplasm, and both domains are tethered via an intrinsically disordered region that traverses the periplasm. Phylogenetic analyses reveal that the Dma family is a unique feature of Bacteroidota. This study provides the first mechanistic insights into the regulation of OMV biogenesis in human gut bacteria.
Collapse
|
34
|
Lynch JB, Gonzalez EL, Choy K, Faull KF, Jewell T, Arellano A, Liang J, Yu KB, Paramo J, Hsiao EY. Gut microbiota Turicibacter strains differentially modify bile acids and host lipids. Nat Commun 2023; 14:3669. [PMID: 37339963 DOI: 10.1038/s41467-023-39403-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
Bacteria from the Turicibacter genus are prominent members of the mammalian gut microbiota and correlate with alterations in dietary fat and body weight, but the specific connections between these symbionts and host physiology are poorly understood. To address this knowledge gap, we characterize a diverse set of mouse- and human-derived Turicibacter isolates, and find they group into clades that differ in their transformations of specific bile acids. We identify Turicibacter bile salt hydrolases that confer strain-specific differences in bile deconjugation. Using male and female gnotobiotic mice, we find colonization with individual Turicibacter strains leads to changes in host bile acid profiles, generally aligning with those produced in vitro. Further, colonizing mice with another bacterium exogenously expressing bile-modifying genes from Turicibacter strains decreases serum cholesterol, triglycerides, and adipose tissue mass. This identifies genes that enable Turicibacter strains to modify host bile acids and lipid metabolism, and positions Turicibacter bacteria as modulators of host fat biology.
Collapse
Affiliation(s)
- Jonathan B Lynch
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Erika L Gonzalez
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kayli Choy
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kym F Faull
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | | | | | - Kristie B Yu
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jorge Paramo
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine Y Hsiao
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| |
Collapse
|
35
|
Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL. Infection leaves a genetic and functional mark on the gut population of a commensal bacterium. Cell Host Microbe 2023; 31:811-826.e6. [PMID: 37119822 PMCID: PMC10197903 DOI: 10.1016/j.chom.2023.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/04/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Gastrointestinal infection changes microbiome composition and gene expression. In this study, we demonstrate that enteric infection also promotes rapid genetic adaptation in a gut commensal. Measurements of Bacteroides thetaiotaomicron population dynamics within gnotobiotic mice reveal that these populations are relatively stable in the absence of infection, and the introduction of the enteropathogen Citrobacter rodentium reproducibly promotes rapid selection for a single-nucleotide variant with increased fitness. This mutation promotes resistance to oxidative stress by altering the sequence of a protein, IctA, that is essential for fitness during infection. We identified commensals from multiple phyla that attenuate the selection of this variant during infection. These species increase the levels of vitamin B6 in the gut lumen. Direct administration of this vitamin is sufficient to significantly reduce variant expansion in infected mice. Our work demonstrates that a self-limited enteric infection can leave a stable mark on resident commensal populations that increase fitness during infection.
Collapse
Affiliation(s)
- Caroline Tawk
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Natasha A Bencivenga-Barry
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hannah J Lees
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruben J F Ramos
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Justin Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
36
|
Sartorio MG, Pardue EJ, Scott NE, Feldman MF. Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535451. [PMID: 37066189 PMCID: PMC10104005 DOI: 10.1101/2023.04.03.535451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Extracellular vesicles (EV) are produced in all three domains of life, and their biogenesis have common ancient origins in eukaryotes and archaea. Although bacterial vesicles were discovered several decades ago and multiple roles have been attributed to them, no mechanism has been established for vesicles biogenesis in bacteria. For this reason, there is a significant level of skepticism about the biological relevance of bacterial vesicles. In Bacteroides thetaiotaomicron ( Bt ), a prominent member of the human intestinal microbiota, outer membrane vesicles (OMVs) have been proposed to play key physiological roles. By employing outer membrane- and OMV-specific markers fused to fluorescent proteins we visualized OMV biogenesis in live-cells. We performed comparative proteomic analyses to demonstrate that Bt actively tailors its vesicle cargo to optimize the breakdown of diet- and host-derived complex glycans. Surprisingly, our data suggests that OMV are not employed for mucin degradation. We also show that, in Bt , a negatively-charged N-terminal motif acts as a signal for protein sorting into OMVs irrespective of the nutrient availability. We conclude that OMVs are the result of an exquisitely orchestrated mechanism. This work lays the foundation for further investigations into the physiological relevance of OMVs and their roles in gut homeostasis. Furthermore, our work constitutes a roadmap to guide EV biogenesis research in other bacteria.
Collapse
|
37
|
Krishna Kumar R, Foster KR. 3D printing of microbial communities: A new platform for understanding and engineering microbiomes. Microb Biotechnol 2023; 16:489-493. [PMID: 36511313 PMCID: PMC9948180 DOI: 10.1111/1751-7915.14168] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022] Open
Abstract
3D printing has emerged as a powerful way to produce complex materials on-demand. These printing technologies are now being applied in microbiology, with many recent examples where microbes and matrices are co-printed to create bespoke living materials. Here, we propose a new paradigm for microbial printing. In addition to its importance for materials, we argue that printing can be used to understand and engineer microbiome communities, analogous to its use in human tissue engineering. Many microbes naturally live in diverse, spatially structured communities that are challenging to study and manipulate. 3D printing offers an exciting new solution to these challenges, as it can precisely arrange microbes in 3D space, allowing one to build custom microbial communities for a wide range of purposes in research, medicine, and industry.
Collapse
Affiliation(s)
- Ravinash Krishna Kumar
- Centre for Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, UK.,Department of Chemistry, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biochemistry, University of Oxford, Oxford, UK.,Department of Biology, University of Oxford, Oxford, UK
| |
Collapse
|
38
|
Madzak C, Poiret S, Salomé Desnoulez S, Foligné B, Lafont F, Daniel C. Study of the persistence and dynamics of recombinant mCherry-producing Yarrowia lipolytica strains in the mouse intestine using fluorescence imaging. Microb Biotechnol 2023; 16:618-631. [PMID: 36541039 PMCID: PMC9948224 DOI: 10.1111/1751-7915.14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Yarrowia lipolytica is a dimorphic oleaginous non-conventional yeast widely used as a powerful host for expressing heterologous proteins, as well as a promising source of engineered cell factories for various applications. This microorganism has a documented use in Feed and Food and a GRAS (generally recognized as safe) status. Moreover, in vivo studies demonstrated a beneficial effect of this yeast on animal health. However, despite the focus on Y. lipolytica for the industrial manufacturing of heterologous proteins and for probiotic effects, its potential for oral delivery of recombinant therapeutic proteins has seldom been evaluated in mammals. As the first steps towards this aim, we engineered two Y. lipolytica strains, a dairy strain and a laboratory strain, to produce the model fluorescent protein mCherry. We demonstrated that both Y. lipolytica strains transiently persisted for at least 1 week after four daily oral administrations and they maintained the active expression of mCherry in the mouse intestine. We used confocal microscopy to image individual Y. lipolytica cells of freshly collected intestinal tissues. They were found essentially in the lumen and they were rarely in contact with epithelial cells while transiting through the ileum, caecum and colon of mice. Taken as a whole, our results have shown that fluorescent Y. lipolytica strains constitute novel tools to study the persistence and dynamics of orally administered yeasts which could be used in the future as oral delivery vectors for the secretion of active therapeutic proteins in the gut.
Collapse
Affiliation(s)
- Catherine Madzak
- INRAE, AgroParisTech, Paris-Saclay University, UMR 782 SayFood, Thiverval-Grignon, France
| | - Sabine Poiret
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
| | - Sophie Salomé Desnoulez
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Benoit Foligné
- Univ. Lille, INSERM, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France.,Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Catherine Daniel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
| |
Collapse
|
39
|
Hoces D, Greter G, Arnoldini M, Stäubli ML, Moresi C, Sintsova A, Berent S, Kolinko I, Bansept F, Woller A, Häfliger J, Martens E, Hardt WD, Sunagawa S, Loverdo C, Slack E. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 2023; 12:81212. [PMID: 36757366 PMCID: PMC10014078 DOI: 10.7554/elife.81212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/08/2023] [Indexed: 02/10/2023] Open
Abstract
Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B.theta shows a longer lag phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.
Collapse
Affiliation(s)
- Daniel Hoces
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Giorgia Greter
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Melanie L Stäubli
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Claudia Moresi
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Sara Berent
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Isabel Kolinko
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Florence Bansept
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Aurore Woller
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Janine Häfliger
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Claude Loverdo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Emma Slack
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| |
Collapse
|
40
|
Dapa T, Wong DP, Vasquez KS, Xavier KB, Huang KC, Good BH. Within-host evolution of the gut microbiome. Curr Opin Microbiol 2023; 71:102258. [PMID: 36608574 PMCID: PMC9993085 DOI: 10.1016/j.mib.2022.102258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Gut bacteria inhabit a complex environment that is shaped by interactions with their host and the other members of the community. While these ecological interactions have evolved over millions of years, mounting evidence suggests that gut commensals can evolve on much shorter timescales as well, by acquiring new mutations within individual hosts. In this review, we highlight recent progress in understanding the causes and consequences of short-term evolution in the mammalian gut, from experimental evolution in murine hosts to longitudinal tracking of human cohorts. We also discuss new opportunities for future progress by expanding the repertoire of focal species, hosts, and surrounding communities, and by combining deep-sequencing technologies with quantitative frameworks from population genetics.
Collapse
Affiliation(s)
- Tanja Dapa
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Daniel Pgh Wong
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
41
|
Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
Collapse
|
42
|
Modesto JL, Pearce VH, Townsend GE. Harnessing gut microbes for glycan detection and quantification. Nat Commun 2023; 14:275. [PMID: 36650134 PMCID: PMC9845299 DOI: 10.1038/s41467-022-35626-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Glycans facilitate critical biological functions and control the mammalian gut microbiota composition by supplying differentially accessible nutrients to distinct microbial subsets. Therefore, identifying unique glycan substrates that support defined microbial populations could inform therapeutic avenues to treat diseases via modulation of the gut microbiota composition and metabolism. However, examining heterogeneous glycan mixtures for individual microbial substrates is hindered by glycan structural complexity and diversity, which presents substantial challenges to glycomics approaches. Fortuitously, gut microbes encode specialized sensor proteins that recognize unique glycan structures and in-turn activate predictable, specific, and dynamic transcriptional responses. Here, we harness this microbial machinery to indicate the presence and abundance of compositionally similar, yet structurally distinct glycans, using a transcriptional reporter we develop. We implement these tools to examine glycan mixtures, isolate target molecules for downstream characterization, and quantify the recovered products. We assert that this toolkit could dramatically enhance our understanding of the mammalian intestinal environment and identify host-microbial interactions critical for human health.
Collapse
Affiliation(s)
- Jennifer L Modesto
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Victoria H Pearce
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Guy E Townsend
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA. .,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA. .,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA.
| |
Collapse
|
43
|
Midani FS, David LA. Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity. Front Microbiol 2023; 13:910390. [PMID: 36687598 PMCID: PMC9849913 DOI: 10.3389/fmicb.2022.910390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/29/2022] [Indexed: 01/07/2023] Open
Abstract
Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances.
Collapse
Affiliation(s)
- Firas S. Midani
- Center for Genomic and Computational Biology, Duke University, Durham, NC, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Lawrence A. David
- Center for Genomic and Computational Biology, Duke University, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| |
Collapse
|
44
|
Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
Collapse
Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rebecca N Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sophie Jean Walton
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Katherine S Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| |
Collapse
|
45
|
Robinson CM, Short NE, Riglar DT. Achieving spatially precise diagnosis and therapy in the mammalian gut using synthetic microbial gene circuits. Front Bioeng Biotechnol 2022; 10:959441. [PMID: 36118573 PMCID: PMC9478464 DOI: 10.3389/fbioe.2022.959441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian gut and its microbiome form a temporally dynamic and spatially heterogeneous environment. The inaccessibility of the gut and the spatially restricted nature of many gut diseases translate into difficulties in diagnosis and therapy for which novel tools are needed. Engineered bacterial whole-cell biosensors and therapeutics have shown early promise at addressing these challenges. Natural and engineered sensing systems can be repurposed in synthetic genetic circuits to detect spatially specific biomarkers during health and disease. Heat, light, and magnetic signals can also activate gene circuit function with externally directed spatial precision. The resulting engineered bacteria can report on conditions in situ within the complex gut environment or produce biotherapeutics that specifically target host or microbiome activity. Here, we review the current approaches to engineering spatial precision for in vivo bacterial diagnostics and therapeutics using synthetic circuits, and the challenges and opportunities this technology presents.
Collapse
Affiliation(s)
| | | | - David T. Riglar
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
46
|
Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell 2022; 185:3263-3277.e15. [PMID: 35931082 PMCID: PMC9464905 DOI: 10.1016/j.cell.2022.06.050] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/15/2022] [Accepted: 06/25/2022] [Indexed: 12/26/2022]
Abstract
Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent. Native E. coli strains isolated from mouse stool are genetically engineered for long-term engraftment in the conventional mouse gut and enable long-term systemic effects on the host, such as improvements in insulin sensitivity in mouse models of type 2 diabetes.
Collapse
Affiliation(s)
- Baylee J Russell
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steven D Brown
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole Siguenza
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irene Mai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand R Saran
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica S Maissy
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ana C Dantas Machado
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Concepcion Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yukiko Miyamoto
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel B Ho
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA
| | - Lars Eckmann
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
47
|
Abstract
Bacteroides species are prominent members of the human gut microbiota. The prevalence and stability of Bacteroides in humans make them ideal candidates to engineer as programmable living therapeutics. Here we report a biotic decision-making technology in a community of Bacteroides (consortium transcriptional programming) with genetic circuit compression. Circuit compression requires systematic pairing of engineered transcription factors with cognate regulatable promoters. In turn, we demonstrate the compression workflow by designing, building, and testing all fundamental two-input logic gates dependent on the inputs isopropyl-β-D-1-thiogalactopyranoside and D-ribose. We then deploy complete sets of logical operations in five human donor Bacteroides, with which we demonstrate sequential gain-of-function control in co-culture. Finally, we couple transcriptional programs with CRISPR interference to achieve loss-of-function regulation of endogenous genes-demonstrating complex control over community composition in co-culture. This work provides a powerful toolkit to program gene expression in Bacteroides for the development of bespoke therapeutic bacteria.
Collapse
|
48
|
Lai Y, Hayashi N, Lu TK. Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology. Curr Opin Chem Biol 2022; 70:102178. [PMID: 35759819 DOI: 10.1016/j.cbpa.2022.102178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/29/2022]
Abstract
The role of the microbiome in health and disease is attracting the attention of researchers seeking to engineer microorganisms for diagnostic and therapeutic applications. Recent progress in synthetic biology may enable the dissection of host-microbiota interactions. Sophisticated genetic circuits that can sense, compute, memorize, and respond to signals have been developed for the stable commensal bacterium Bacteroides thetaiotaomicron, dominant in the human gut. In this review, we highlight recent advances in expanding the genetic toolkit for B. thetaiotaomicron and foresee several applications of this species for microbiome engineering. We provide our perspective on the challenges and future opportunities for the engineering of human gut-associated bacteria as living therapeutic agents.
Collapse
Affiliation(s)
- Yong Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Senti Biosciences, 2 Corporate Drive South San Francisco, CA 94080, USA.
| |
Collapse
|
49
|
Segura Munoz RR, Mantz S, Martínez I, Li F, Schmaltz RJ, Pudlo NA, Urs K, Martens EC, Walter J, Ramer-Tait AE. Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes. THE ISME JOURNAL 2022; 16:1594-1604. [PMID: 35210551 PMCID: PMC9122919 DOI: 10.1038/s41396-022-01208-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/03/2021] [Accepted: 02/01/2022] [Indexed: 01/07/2023]
Abstract
It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation.
Collapse
Affiliation(s)
- Rafael R Segura Munoz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sara Mantz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Ines Martínez
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Robert J Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, Canada. .,APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland.
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA. .,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
| |
Collapse
|
50
|
Rangarajan AA, Chia HE, Azaldegui CA, Olszewski MH, Pereira GV, Koropatkin NM, Biteen JS. Ruminococcus bromii enables the growth of proximal Bacteroides thetaiotaomicron by releasing glucose during starch degradation. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35471195 DOI: 10.1099/mic.0.001180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Complex carbohydrates shape the gut microbiota, and the collective fermentation of resistant starch by gut microbes positively affects human health through enhanced butyrate production. The keystone species Ruminococcus bromii (Rb) is a specialist in degrading resistant starch; its degradation products are used by other bacteria including Bacteroides thetaiotaomicron (Bt). We analysed the metabolic and spatial relationships between Rb and Bt during potato starch degradation and found that Bt utilizes glucose that is released from Rb upon degradation of resistant potato starch and soluble potato amylopectin. Additionally, we found that Rb produces a halo of glucose around it when grown on solid media containing potato amylopectin and that Bt cells deficient for growth on potato amylopectin (∆sus Bt) can grow within the halo. Furthermore, when these ∆sus Bt cells grow within this glucose halo, they have an elongated cell morphology. This long-cell phenotype depends on the glucose concentration in the solid media: longer Bt cells are formed at higher glucose concentrations. Together, our results indicate that starch degradation by Rb cross-feeds other bacteria in the surrounding region by releasing glucose. Our results also elucidate the adaptive morphology of Bt cells under different nutrient and physiological conditions.
Collapse
Affiliation(s)
| | - Hannah E Chia
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Monica H Olszewski
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gabriel V Pereira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|